altere setTimeout com isso:
setTimeout(function(){countdown(theyear,themonth,theday,id);},1000)
você pode fazer sua função para jQuery funcionar assim:
jQuery.fn.countdown = function(yr,m,d){
$that = $(this);
theyear=yr;themonth=m;theday=d
var today=new Date()
var todayy=today.getYear()
if (todayy < 1000)
todayy+=1900
var todaym=today.getMonth()
var todayd=today.getDate()
var todayh=today.getHours()
var todaymin=today.getMinutes()
var todaysec=today.getSeconds()
var todaystring=montharray[todaym]+" "+todayd+", "+todayy+" "+todayh+":"+todaymin+":"+todaysec
futurestring=montharray[m-1]+" "+d+", "+yr
dd=Date.parse(futurestring)-Date.parse(todaystring)
dday=Math.floor(dd/(60*60*1000*24)*1)
dhour=Math.floor((dd%(60*60*1000*24))/(60*60*1000)*1)
dmin=Math.floor(((dd%(60*60*1000*24))%(60*60*1000))/(60*1000)*1)
dsec=Math.floor((((dd%(60*60*1000*24))%(60*60*1000))%(60*1000))/1000*1)
if(dday==0 && dhour==0 && dmin==0 && dsec==0){
$that.val(current);
return
}
else
$that.val("Only "+dday+ " days, "+dhour+" hours, "+dmin+" minutes, and "+dsec+" seconds left "+before);
setTimeout(function(){ $that.countdown(theyear,themonth,theday);},1000)
}
<?php
include('../connection.php');
$rs = mysql_query("select * from datepic") or die(mysql_error());
if(mysql_num_rows($rs)){
while($row = mysql_fetch_array($rs))
{
$date = str_replace('-',',',$row['date']);
echo '<input type="text" id="'.$row['id'].'" size=80>';
?>
<script>
$("?php echo $row['id'] ?>").countdown(<?php echo $date?>);
</script>
<?php
}
}
?>
